Genomic features associated with sustained mammalian transmission of avian influenza A viruses.

Abstract

Comparably few lineages of influenza A virus (IAV) have evolved long-term sustained transmission in mammals. The reasons remain largely unknown, and the possibility of avian IAVs evolving sustained mammalian transmission is an ongoing concern. Here we measured the GC content and frequency of GC dinucleotides in 115,520 whole genomes of IAVs using bioinformatic analyses. We found that persistent mammalian lineages showed declining trends in GC-related content and could be reliably separated from IAVs circulating only in birds and those sporadically infecting mammals. Similarly, the earliest viruses of persistent mammalian lineages showed reduced GC-related content, suggesting that this trait might in part contribute to their eventual persistence. Recent highly pathogenic 2.3.4.4b H5 viruses that spread in mink, foxes and humans were also characterized by reduced GC-related content. While not sufficient, reduced GC-related content may be a necessary condition for sustained mammalian transmission and should be included in risk assessment tools for pandemic influenza.